23 - RF-selected LV Genomic Variant Test
Sara Gosline
2019-11-26
Get Data
This is nearly entirely based on the code in notebook 09 and that in 11.
We have latent variable expression analysis data - Latent Variable Table
For this data we are also using any data for which there are gene variants (cNFs, pNFs, MPNSTs): - Exome-Seq variants - WGS Variants
Let’s see if there are any LVs that split based on gene variant. Because we’re having trouble scaling with the number of latent variables, I only look at variants that occur in less than 5% of the population. notice this is a difference from notebook #11.
wgs.vars=synTableQuery("SELECT Hugo_Symbol,Protein_position,specimenID,IMPACT,FILTER,ExAC_AF,gnomAD_AF FROM syn20551862")$asDataFrame()##
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Downloading [####################]100.00% 82.5MB/82.5MB (10.6MB/s) Job-10312797222738272612269072.csv Done...all.vars<-rbind(select(wgs.vars,'Hugo_Symbol','Protein_position','specimenID','IMPACT','gnomAD_AF'),
select(exome.vars,'Hugo_Symbol','Protein_position','specimenID','IMPACT','gnomAD_AF'))%>%
subset(gnomAD_AF<0.01)
top.lvs<-synTableQuery("SELECT * from syn21318452")$asDataFrame()##
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filter(isCellLine != "TRUE")%>%
subset(latent_var%in%top.lvs$LatentVar)%>%
select(latent_var,id,value,specimenID,tumorType,modelOf,diagnosis)##
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Downloading [####################]100.00% 25.1MB/25.1MB (5.4MB/s) Job-103128005765236745870494946.csv Done...Merge data together
For the purposes of this analysis we want to have only those samples wtih genomic data and only those latent variables that are highly variable.
samps<-intersect(mp_res$specimenID,all.vars$specimenID)
mp_res<-mp_res%>%
subset(specimenID%in%samps)#%>%
# group_by(latent_var) %>%
# mutate(sd_value = sd(value)) %>%
# filter(sd_value > 0.025) %>%
# ungroup()Retrieve Variant Data
Let’s retrieve the LV data and evaluate any correlations between scores and tumor size or patient age
data.with.var<-mp_res%>%subset(specimenID%in%samps)%>%
left_join(all.vars,by='specimenID')
tab<-subset(data.with.var,!tumorType%in%c('Other','High Grade Glioma','Low Grade Glioma'))
top.genes=tab%>%#group_by(tumorType)%>%
mutate(numSamps=n_distinct(specimenID))%>%
group_by(Hugo_Symbol)%>%
mutate(numMutated=n_distinct(specimenID))%>%
ungroup()%>%
subset(numMutated>2)%>%
subset(numMutated<(numSamps-2))%>%
select(tumorType,Hugo_Symbol,numSamps,numMutated)%>%distinct()
gene.count=top.genes%>%group_by(tumorType)%>%mutate(numGenes=n_distinct(Hugo_Symbol))%>%select(tumorType,numGenes)%>%distinct()
DT::datatable(gene.count)Now we can loop through every tumor type and gene
red.genes<-c("NF1","SUZ12","CDKN2A","EED")##for testing
##first spread the WT/Mutated values
vals<-tab%>%subset(Hugo_Symbol%in%top.genes$Hugo_Symbol)%>%
mutate(mutated=ifelse(is.na(IMPACT),'WT','Mutated'))%>%
select(latent_var,tumorType,value,Hugo_Symbol,specimenID,mutated)%>%
distinct()%>%
spread(key=Hugo_Symbol,value='mutated',fill='WT')
##double check to make sure there are both mutated and unmutated values
counts<-vals%>%
gather(key=gene,value=status,-c(latent_var,tumorType,value,specimenID))%>%
select(latent_var,tumorType,value,gene,specimenID,status)%>%
group_by(latent_var,gene)%>%
mutate(numVals=n_distinct(status))%>%
mutate(numSamps=n_distinct(specimenID))%>%
subset(numVals==2)%>%ungroup()
#so now we have only
with.sig<-counts%>%ungroup()%>%#subset(gene%in%top.genes$Hugo_Symbol)%>%
group_by(latent_var,gene)%>%
mutate(pval=t.test(value~status)$p.value)%>%ungroup()%>%
group_by(latent_var)%>%
mutate(corP=p.adjust(pval))%>%ungroup()%>%
select(latent_var,gene,pval,corP)%>%distinct()
sig.vals<-subset(with.sig,corP<0.01)
DT::datatable(sig.vals)Interesting! Some genes actually pass p-value correction. What do they look like? Here let’s write the messiest possible code to print.
for(ct in unique(sig.vals$latent_var)){
tplot<-sig.vals[which(sig.vals$latent_var==ct),]
if(nrow(tplot)==0)
next
print(ct)
sigs=tplot%>%rowwise()%>%mutate(vals=paste(gene,format(corP,digits=3),sep=':'))%>%select(vals)%>%unlist()%>%paste(collapse=',')
print(sigs)
p<-counts%>%
subset(latent_var==ct)%>%
subset(gene%in%tplot$gene)%>%
ggplot(aes(x=gene,y=value,col=status))+
geom_boxplot(outlier.shape=NA)+
geom_point(position=position_jitterdodge(),aes(shape=tumorType,group=status))+
theme(axis.text.x = element_text(angle = 90, hjust = 1))+
ggtitle(paste(ct,'scores\n',sigs))
# if(method=='cibersort')
# p<-p+scale_y_log10()
print(p)
}## [1] "451,REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT"
## [1] "AAAS:1.74e-05,AADAC:1.74e-05,AFAP1:1.74e-05,AIPL1:1.74e-05,AL050302.1:7.56e-06,ANKRD20A1:7.56e-06,ANKRD34C:1.74e-05,ANKRD36:9.01e-05,ANKRD36C:6.71e-05,ANP32B:9.8e-06,APOM:1.74e-05,AQP7:2.74e-05,ARHGEF33:1.74e-05,ARHGEF39:1.74e-05,ATOH1:1.74e-05,B4GALT7:1.74e-05,BIK:1.74e-05,C11orf86:1.74e-05,C19orf54:1.74e-05,C1orf174:1.74e-05,CA7:1.74e-05,CACNA1C:1.74e-05,CAPN7:1.74e-05,CATSPERG:1.74e-05,CCDC144NL:6.48e-05,CCDC64B:1.74e-05,CD300LD:1.74e-05,CDC27:7.56e-06,CDH9:1.74e-05,CETN1:1.74e-05,CHD1L:1.74e-05,CHRNB2:1.74e-05,CLSTN1:1.74e-05,CMTM3:1.74e-05,CNN2:0.00246,CPB1:1.74e-05,CTBP2:6.15e-05,CTDSP2:7.56e-06,CTPS2:1.74e-05,CTTN:1.74e-05,CUZD1:1.74e-05,DBN1:1.74e-05,DHDH:1.74e-05,EIF4G3:1.74e-05,ENO1:1.74e-05,FAM104B:7.56e-06,FAM182B:7.56e-06,FAM227B:8.47e-08,FAM83B:1.74e-05,FGD2:1.74e-05,FRG1B:7.56e-06,FUT2:0.00542,GGT1:3.55e-05,GJA10:1.74e-05,GLG1:1.74e-05,GNB1L:0.00125,GUCY2C:1.74e-05,HEYL:1.74e-05,HK3:1.74e-05,HNRNPCL1:7.56e-06,HYDIN:9.3e-06,IGHG4:1.74e-05,IGLV2-8:1.74e-05,IGSF3:7.56e-06,IL18:1.74e-05,INO80D:1.74e-05,INSRR:1.74e-05,ITGB7:1.74e-05,ITIH6:1.74e-05,KAZN:1.74e-05,KCTD16:1.74e-05,KIAA0391:1.74e-05,KIAA1239:1.74e-05,KIF18A:1.74e-05,KRT18:0.00578,KRTAP5-4:8.47e-08,KRTCAP3:1.74e-05,LEPROT:1.74e-05,LRP2BP:1.74e-05,LRRC10:1.74e-05,LRRIQ4:1.74e-05,LY6G6C:1.74e-05,LY6H:1.74e-05,MUC12:0.0011,MUC3A:4.89e-06,MUC6:0.000667,MYO1C:1.74e-05,MYRIP:1.74e-05,NPIPB11:9.68e-08,NPLOC4:1.74e-05,OLIG1:1.74e-05,OR10H3:1.74e-05,OR2M5:1.74e-05,OR4C5:4.06e-05,OR5B17:1.74e-05,OR8U1:6.4e-05,P2RX6:1.74e-05,PABPC3:0.00439,PCDHB14:1.74e-05,PDYN:1.74e-05,PDZD7:1.74e-05,PGA3:1.74e-05,PGM5:1.74e-05,POTED:0.000853,PRAMEF2:2.35e-05,PRPH:1.74e-05,PRRG2:1.74e-05,PRSS1:0.00485,PRSS3:7.56e-06,PTK2B:1.74e-05,PXN:1.74e-05,QSOX2:1.74e-05,RACGAP1:1.74e-05,RAD21L1:1.74e-05,RP9:1.74e-05,S1PR3:1.74e-05,SEL1L3:1.74e-05,SHOX:1.74e-05,SLC25A5:7.56e-06,SPAST:1.74e-05,SPESP1:1.74e-05,SPINT2:1.74e-05,STK32A:1.74e-05,TAS2R19:7.56e-06,TAS2R31:7.56e-06,TAS2R43:0.000195,THEM6:1.74e-05,TMEM168:1.74e-05,TMEM2:0.00291,TMEM53:1.74e-05,TNFRSF4:1.74e-05,TNFRSF6B:1.74e-05,TRBV10-1:7.56e-06,TRBV7-3:7.56e-06,TRMT2B:1.74e-05,TTBK1:1.74e-05,TXNDC17:1.74e-05,TYR:1.74e-05,UBXN7:1.74e-05,UMPS:1.74e-05,UNC5CL:1.74e-05,UPF2:1.74e-05,ZDHHC7:1.74e-05,ZMYM3:1.74e-05,ZNF717:7.56e-06,ZNF76:0.00521"
## [1] "LV 420"
## [1] "ABCB1:0.00153,ANKRD7:0.00153,AP001024.1:0.00153,ATXN2:0.000491,C16orf3:0.00153,C17orf53:0.00153,C9orf131:0.00153,CC2D1A:0.00153,CCDC169-SOHLH2:0.00153,CD209:0.00775,CEACAM5:0.000217,CNKSR1:0.00153,COL4A3BP:0.00425,DCTN1:0.00741,DENND4A:0.00153,DNASE2B:0.00153,FAM181B:0.00153,FANCC:0.00153,FBP1:0.00153,GCOM1:0.00153,HDAC9:0.00153,HUS1B:0.00153,IFNAR2:0.00425,IFNGR2:0.00153,INTS4:0.00153,KRT81:0.00153,KRTAP4-6:0.000491,MSH6:0.00741,MYOF:0.00425,NCSTN:0.00153,NEK11:0.00153,NOL12:0.00153,OR51G1:0.00153,PARPBP:0.00153,PLXNC1:0.00153,PMF1-BGLAP:0.00153,PPP1R37:0.00153,PRKCSH:0.00741,PYGM:0.00153,RAD54B:0.00153,RAMP3:0.00153,SLC35D2:0.00153,SMARCC2:0.000491,SNX21:0.00153,TADA2A:0.00153,TTI2:0.000503,UPF3A:0.00153,ZNF157:0.00153,ZNF37A:0.00153,ZNF532:0.00741,ZNF541:0.00153,ZNF90:0.00153"
## [1] "LV 849"
## [1] "ABCC12:0.000486,ADAMTS20:2.72e-06,AL050302.1:6.41e-05,ANKRD20A1:6.41e-05,ANKRD36:0.00737,ANP32B:0.00258,ART1:0.000442,ART3:0.00109,ASB18:4.43e-06,ATAD3C:0.00643,ATP10B:2.72e-06,CCDC144NL:0.00162,CDC27:6.41e-05,CLDN8:0.00941,CSGALNACT1:0.00514,CTBP2:0.00241,CTDSP2:6.41e-05,DAB2IP:2.72e-06,DIP2A:2.72e-06,EFCAB12:0.00514,FAM104B:6.41e-05,FAM182B:6.41e-05,FAM212A:0.00941,FRG1B:6.41e-05,GGT1:0.00171,GRIK4:2.72e-06,GSDMB:2.72e-06,GSDMD:2.72e-06,GTF3A:0.000706,HNRNPCL1:6.41e-05,HYDIN:0.00163,IGSF3:6.41e-05,ILDR1:0.00643,INMT:2.72e-06,KCNK5:2.72e-06,KCTD8:0.00155,KIAA1211:2.72e-06,MUC15:0.000486,MUC3A:0.00142,NPIPB15:0.00138,NR5A2:0.00643,OMA1:0.00342,OR4M2:0.00893,OR5AU1:2.72e-06,PCBP4:0.00342,PHRF1:0.000488,PLA2G4C:0.00643,POTED:0.00164,PRKCQ:0.00739,PRSS3:6.41e-05,RHOT2:2.72e-06,RP11-766F14.2:8.05e-05,SEC14L4:0.00833,SERPINB11:0.00941,SLC25A5:6.41e-05,TAS2R19:6.41e-05,TAS2R31:6.41e-05,TBC1D31:2.72e-06,TCF20:8.21e-06,TRBV10-1:6.41e-05,TRBV7-3:6.41e-05,UMODL1:9.65e-05,USP19:0.00941,USP4:0.00941,USP43:0.000752,VPS13C:9.57e-07,ZNF717:6.41e-05"
## [1] "LV 185"
## [1] "ABCF1:5.94e-05,AL050302.1:0.00049,ANKRD20A1:0.00049,ANKRD36:0.00683,ANP32B:0.00125,CCDC144NL:8.56e-05,CDC27:0.00049,CTBP2:0.00256,CTDSP2:0.00049,FAM104B:0.00049,FAM182B:0.00049,FRG1B:0.00049,GGT1:0.00203,HNRNPCL1:0.00049,HYDIN:0.00235,IGSF3:0.00049,MDM1:3.29e-08,MUC3A:0.00225,OR8U1:0.000143,POTED:0.00375,PRAMEF2:0.000796,PRSS3:0.00049,SLC25A5:0.00049,TAS2R19:0.00049,TAS2R31:0.00049,TENM3:1.85e-08,TRBV10-1:0.00049,TRBV7-3:0.00049,ZNF717:0.00049"
## [1] "LV 521"
## [1] "AC187652.1:0.00184"
## [1] "1,REACTOME_MRNA_SPLICING"
## [1] "ADAMTSL3:0.00156,AIRE:0.00156,ANKRD18A:0.00156,ANKRD31:0.00139,APBB1IP:0.00224,CEP350:0.00224,CEP85L:0.00156,COL5A2:0.000439,CORO7:0.00156,CPNE3:0.000463,CPS1:0.000463,DDI1:0.0041,DUSP15:0.00446,FAM175A:0.0069,FDXR:0.00228,GLI2:0.000536,HIBCH:0.00722,KLHL38:0.00156,KRTAP4-16P:0.00446,NUMBL:0.00602,NUP133:0.000463,OR2S2:0.00156,PPFIA4:0.000834,PRRC2A:0.000463,REEP3:0.00139,RESP18:0.00156,RIN1:0.00141,SHC2:0.00156,SLC1A7:0.0022,SLC7A14:0.00321,TAS1R1:0.00157,TICRR:0.00409,WDR76:0.00139,ZNF862:0.00156,ZNF93:0.0046"
## [1] "4,REACTOME_NEURONAL_SYSTEM"
## [1] "AL050302.1:0.000757,ANKRD20A1:0.000757,AQP7:0.00183,C1orf51:5.16e-08,CCDC144NL:0.00138,CDC27:0.000757,CTBP2:0.000824,CTDSP2:0.000757,FAM104B:0.000757,FAM182B:0.000757,FRG1B:0.000757,GGT1:0.00182,HNRNPCL1:0.000757,HYDIN:0.00706,IGSF3:0.000757,MUC3A:0.00801,POTED:0.00611,PRSS1:0.000749,PRSS3:0.000757,SLC25A5:0.000757,TAS2R19:0.000757,TAS2R31:0.000757,TRBV10-1:0.000757,TRBV7-3:0.000757,UNC13D:8.26e-07,ZNF717:0.000757"
## [1] "LV 308"
## [1] "AL050302.1:3.26e-05,ANKRD20A1:3.26e-05,ANKRD36:0.000713,ANKRD36C:0.00888,ANP32B:0.000242,AQP7:6.1e-05,CCDC144NL:0.000906,CDC27:3.26e-05,CTBP2:9.9e-05,CTDSP2:3.26e-05,EPOR:0.00094,FAM104B:3.26e-05,FAM170A:2.64e-06,FAM182B:3.26e-05,FRG1B:3.26e-05,GGT1:0.00417,HNRNPCL1:3.26e-05,HYDIN:0.000608,IGSF3:3.26e-05,MUC12:0.000899,MUC3A:0.00123,MUC6:0.00358,OR4C5:0.000147,OR8U1:0.00499,POTED:0.0031,PRSS1:0.00173,PRSS3:3.26e-05,RP11-231C14.4:2.26e-06,SLC22A31:2.76e-05,SLC25A5:3.26e-05,TAS2R19:3.26e-05,TAS2R31:3.26e-05,TRBV10-1:3.26e-05,TRBV7-3:3.26e-05,UBR4:1.57e-06,ZNF717:3.26e-05"
## [1] "LV 442"
## [1] "AL050302.1:0.00172,ANKRD20A1:0.00172,ANP32B:0.00198,CDC27:0.00172,CTBP2:0.00275,CTDSP2:0.00172,FAM104B:0.00172,FAM175A:0.00114,FAM182B:0.00172,FRG1B:0.00172,GGT1:0.00149,GYS2:0.000896,HNRNPCL1:0.00172,IGSF3:0.00172,KLHL41:0.000412,LRRC17:6e-04,POTED:0.00487,PRSS3:0.00172,SLC1A7:0.0019,SLC25A5:0.00172,SNX19:0.000961,TAS2R19:0.00172,TAS2R31:0.00172,TRBV10-1:0.00172,TRBV7-3:0.00172,ZNF598:0.00411,ZNF717:0.00172,ZNF721:0.000223"
## [1] "LV 445"
## [1] "AL050302.1:0.000145,ANKRD20A1:0.000145,ANKRD36:0.00479,ANP32B:0.0015,AQP7:0.00235,CCDC144NL:0.00471,CDC27:0.000145,CNN2:0.00872,CTBP2:0.0027,CTDSP2:0.000145,FAM104B:0.000145,FAM182B:0.000145,FRG1B:0.000145,GGT1:0.000692,HNRNPCL1:0.000145,HYDIN:0.00123,IGSF3:0.000145,MUC3A:0.000441,NPIPB15:0.00143,POTED:0.000884,PRSS3:0.000145,SLC25A5:0.000145,TAS2R19:0.000145,TAS2R31:0.000145,TRBV10-1:0.000145,TRBV7-3:0.000145,ZNF717:0.000145"
## [1] "LV 492"
## [1] "AL050302.1:0.00993,ANKRD20A1:0.00993,AQP7:0.00212,CDC27:0.00993,CTDSP2:0.00993,FAM104B:0.00993,FAM182B:0.00993,FRG1B:0.00993,HNRNPCL1:0.00993,HYDIN:0.00264,IGSF3:0.00993,MUC12:0.000115,MUC6:0.000174,OR4C5:1.57e-05,PRSS3:0.00993,SLC25A5:0.00993,TAS2R19:0.00993,TAS2R31:0.00993,TRBV10-1:0.00993,TRBV7-3:0.00993,ZNF717:0.00993"
## [1] "LV 635"
## [1] "AL050302.1:0.00205,ANKRD20A1:0.00205,ANP32B:0.00788,AQP7:0.00366,CCDC144NL:0.00243,CDC27:0.00205,CTBP2:0.00805,CTDSP2:0.00205,FAM104B:0.00205,FAM182B:0.00205,FRG1B:0.00205,HNRNPCL1:0.00205,HYDIN:0.00219,IGSF3:0.00205,MUC12:0.00313,MUC6:0.0027,OR4C5:0.000601,OR8U1:0.00912,PRSS3:0.00205,SLC25A5:0.00205,TAS2R19:0.00205,TAS2R31:0.00205,TRBV10-1:0.00205,TRBV7-3:0.00205,ZNF717:0.00205,ZNF93:0.00864"
## [1] "LV 644"
## [1] "AL050302.1:0.000631,ANKRD20A1:0.000631,AQP7:0.00708,CCDC144NL:0.00215,CDC27:0.000631,CTBP2:0.000513,CTDSP2:0.000631,FAM104B:0.000631,FAM182B:0.000631,FRG1B:0.000631,GNB1L:3.15e-05,HNRNPCL1:0.000631,HYDIN:0.00104,IGSF3:0.000631,MUC3A:0.00277,PIGT:0.0049,POTED:0.0032,PRSS3:0.000631,SLC25A5:0.000631,TAS2R19:0.000631,TAS2R31:0.000631,TRBV10-1:0.000631,TRBV7-3:0.000631,ZNF717:0.000631,ZYX:0.000334"
## [1] "LV 653"
## [1] "AL050302.1:0.000269,ANKRD20A1:0.000269,ANP32B:0.00283,AQP7:0.00832,CCDC144NL:3.06e-05,CDC27:0.000269,COL5A2:1.39e-05,CPNE3:5.52e-05,CPS1:5.52e-05,CTBP2:0.00117,CTDSP2:0.000269,DUSP15:0.00081,FAM104B:0.000269,FAM182B:0.000269,FRG1B:0.000269,GBP4:0.000524,GGT1:0.00669,HNRNPCL1:0.000269,HYDIN:0.00079,IGSF3:0.000269,KRTAP4-16P:0.00081,MUC3A:0.00772,NUP133:5.52e-05,OR4C5:0.0083,OR8U1:0.000311,POTED:0.00235,PRAMEF2:0.00554,PRRC2A:5.52e-05,PRSS3:0.000269,SLC25A5:0.000269,SLC7A14:0.00944,TAS2R19:0.000269,TAS2R31:0.000269,TRBV10-1:0.000269,TRBV7-3:0.000269,ZNF646:0.00113,ZNF717:0.000269,ZNF93:0.00517"
## [1] "LV 665"
## [1] "AL050302.1:5.69e-05,ANKRD20A1:5.69e-05,ANKRD36:0.00745,ANP32B:0.000702,AQP7:0.0086,C16orf71:0.00116,CCDC144NL:0.000233,CD248:0.00118,CDC27:5.69e-05,CTBP2:0.000824,CTDSP2:5.69e-05,DACT2:0.00184,DHODH:0.000584,FAM104B:5.69e-05,FAM182B:5.69e-05,FRG1B:5.69e-05,GGT1:0.00106,GRIP1:0.00116,HNRNPCL1:5.69e-05,HYDIN:0.000358,IGSF3:5.69e-05,KIF26A:0.00194,KIR3DL2:0.00167,LRIG2:0.00149,MUC3A:0.000762,NPIPB15:0.000987,OR8U1:0.00302,PHC3:0.000555,POTED:0.000501,PRSS3:5.69e-05,SH3RF3:0.00575,SLC25A5:5.69e-05,SLC3A1:0.00118,ST6GAL2:0.000467,TAS2R19:5.69e-05,TAS2R31:5.69e-05,TNFRSF21:0.00116,TPBGL:0.00947,TRBV10-1:5.69e-05,TRBV7-3:5.69e-05,TYRP1:0.00116,ZNF717:5.69e-05,ZNF843:0.00116"
## [1] "LV 72"
## [1] "AL050302.1:0.00233,ANKRD20A1:0.00233,CDC27:0.00233,CTDSP2:0.00233,FAM104B:0.00233,FAM182B:0.00233,FRG1B:0.00233,GGT1:0.00674,HNRNPCL1:0.00233,HYDIN:0.00256,IGSF3:0.00233,MUC3A:0.00195,PRSS3:0.00233,SLC25A5:0.00233,TAS2R19:0.00233,TAS2R31:0.00233,TRBV10-1:0.00233,TRBV7-3:0.00233,ZNF717:0.00233"
## [1] "LV 851"
## [1] "AL050302.1:1.64e-06,ANKRD20A1:1.64e-06,ANKRD36:0.000272,ANKRD36C:0.00542,ANP32B:5.83e-05,AQP7:0.000224,C1orf51:0.000371,CCDC144NL:2.77e-05,CDC27:1.64e-06,CENPJ:0.000272,CTBP2:5.1e-06,CTDSP2:1.64e-06,FAM104B:1.64e-06,FAM182B:1.64e-06,FLYWCH1:0.000272,FRG1B:1.64e-06,FTSJ3:0.000465,GGT1:1.02e-05,GLI2:0.00733,HNRNPCL1:1.64e-06,HYDIN:6.5e-05,IGSF3:1.64e-06,MUC3A:2.07e-05,NHS:0.000465,NPIPB15:0.00853,OR8U1:0.000698,POTED:2.41e-05,PRAMEF2:0.0049,PRSS1:0.00982,PRSS3:1.64e-06,RNH1:0.000272,SLC25A5:1.64e-06,TAS2R19:1.64e-06,TAS2R31:1.64e-06,TAS2R43:0.000546,TRBV10-1:1.64e-06,TRBV7-3:1.64e-06,ZNF717:1.64e-06"
## [1] "LV 864"
## [1] "AL050302.1:0.00449,ANKRD20A1:0.00449,CDC27:0.00449,CTDSP2:0.00449,FAM104B:0.00449,FAM182B:0.00449,FRG1B:0.00449,HNRNPCL1:0.00449,IGSF3:0.00449,PRSS3:0.00449,SLC25A5:0.00449,TAS2R19:0.00449,TAS2R31:0.00449,TRBV10-1:0.00449,TRBV7-3:0.00449,ZNF717:0.00449"
## [1] "LV 984"
## [1] "AL050302.1:0.000112,ANKRD20A1:0.000112,ANKRD36:0.00126,ANKRD36C:0.00275,ANP32B:0.000555,AQP7:0.000454,CCDC144NL:0.000225,CDC27:0.000112,CTBP2:0.00148,CTDSP2:0.000112,FAM104B:0.000112,FAM182B:0.000112,FIP1L1:0.00942,FRG1B:0.000112,GBP4:0.00256,GGT1:0.000187,HNRNPCL1:0.000112,HYDIN:0.000403,IGSF3:0.000112,LRIG1:0.00548,MUC12:0.00375,MUC3A:0.000294,MUC6:0.00415,NPIPB15:0.0051,OR4C5:0.00183,OR8U1:0.000843,PABPN1L:0.00949,POTED:0.000446,PRAMEF2:0.0014,PRSS3:0.000112,SLC25A5:0.000112,TAS2R19:0.000112,TAS2R31:0.000112,TAS2R43:0.00232,TRBV10-1:0.000112,TRBV7-3:0.000112,ZNF717:0.000112"
## [1] "LV 751"
## [1] "ANKRD31:0.0019,MFSD2B:0.00091,REEP3:0.0019,WDR76:0.0019"
## [1] "LV 380"
## [1] "ASTN2:0.00272,ATXN7L1:0.00727,MCM5:8.02e-05,MS4A15:0.00035,MUC16:0.000557,MUC2:0.00241,MUC6:6.79e-06,OR6N2:0.000133,ZNF780B:0.00035"
## [1] "LV 816"
## [1] "ATP6AP1:8.33e-07,NDUFC2:0.00142"
## [1] "985,IRIS_Neutrophil-Resting"
## [1] "C13orf35:0.000985,C16orf71:0.0019,C17orf99:0.000985,CERS3:0.000985,GRIP1:0.0019,OR7G3:0.000985,PHC3:0.00315,PODXL:0.000985,PODXL2:0.000985,SLC37A2:0.000985,SPATC1L:0.000985,TNFRSF21:0.0019,TPBGL:0.00101,TYRP1:0.0019,ZCCHC2:0.000985,ZNF510:0.000985,ZNF843:0.0019"
## [1] "LV 957"
## [1] "C1orf51:3.16e-05,UNC13D:0.00809"
## [1] "LV 690"
## [1] "C9orf129:0.00651,CAMSAP1:0.000761,CD248:1.4e-05,IL4I1:0.00235,KIAA0586:0.000225,SLC3A1:1.4e-05"
## [1] "LV 229"
## [1] "CCDC144NL:0.000833,COL5A2:0.00789,OR8U1:0.00722"
## [1] "LV 379"
## [1] "CCDC144NL:0.000938,OR8U1:0.00127"
## [1] "LV 917"
## [1] "CD248:0.00387,FDXR:0.00431,MUC6:0.00556,SLC3A1:0.00387,TICAM1:0.00109,ZNF646:2.19e-05"
## [1] "LV 533"
## [1] "CDC42BPG:0.00228,MUC3A:0.00576,STYK1:0.00228"
## [1] "LV 496"
## [1] "CEP85:0.00339"
## [1] "LV 9"
## [1] "COL5A2:0.00796,FDXR:0.00728,PHF3:0.00615,SCAMP3:0.00713,ZBED6:0.00749"
## [1] "13,REACTOME_GLUCOSE_METABOLISM"
## [1] "CTD-3193O13.9:0.00833,GPR114:0.00833,KIF26A:0.000528,PPP6R2:0.00833,SPG7:0.00865"
## [1] "LV 272"
## [1] "DACT2:0.00183,SH3RF3:0.00158"
## [1] "LV 32"
## [1] "DCBLD2:0.000323,GYLTL1B:2.17e-05,MUC16:0.00305,PPP1R18:9.69e-06,SH3RF3:2.75e-05"
## [1] "LV 484"
## [1] "DGKG:0.00371,EPHX2:0.00371,GTF3A:0.00951,PPP1R13B:0.00422,SDF4:0.00855"
## [1] "LV 303"
## [1] "DYTN:0.00793,SH3RF3:0.00975,ZNF646:1.32e-06"
## [1] "LV 520"
## [1] "GZMA:1.21e-05,TDRD6:0.000135"
## [1] "928,DMAP_ERY3"
## [1] "HBQ1:0.00307,OR8B12:0.00278,VWA3A:0.00278"
## [1] "31,SVM B cells naive"
## [1] "HEXDC:5.59e-05,NT5DC4:5.03e-05,PP2D1:2.9e-05,SERPINA1:0.00252,SSTR5:0.000356,ST6GAL2:2.73e-06"
## [1] "827,KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY"
## [1] "HSF4:3.1e-10"
## [1] "LV 15"
## [1] "HSF4:1.49e-06"
## [1] "LV 88"
## [1] "KCTD8:3.44e-05"
## [1] "LV 94"
## [1] "KDM4D:0.0089"
## [1] "LV 418"
## [1] "KIAA0586:0.00388,RSF1:0.000254"
## [1] "LV 971"
## [1] "METTL17:0.000173"
## [1] "LV 625"
## [1] "MUC16:0.00817"
## [1] "953,IRIS_Monocyte-Day1"
## [1] "NEK5:6.34e-11,NETO2:6.34e-11"
## [1] "97,KEGG_ARACHIDONIC_ACID_METABOLISM"
## [1] "OR8B12:0.00261,VWA3A:0.00261"
## [1] "LV 100"
## [1] "PDHA2:0.000772"
## [1] "LV 624"
## [1] "RP11-231C14.4:0.00722,ZNF93:3.05e-06"
## [1] "LV 909"
## [1] "SCN9A:5.42e-05,UNC13D:0.000218"
## [1] "45,REACTOME_RNA_POL_I_PROMOTER_OPENING"
## [1] "SOX11:0.000229"
## [1] "767,SVM B cells naive"
## [1] "TPSD1:0.00676,ZNF462:0.000111"
## [1] "LV 376"
## [1] "ZNF93:3.97e-05"
#}Breaking down by tumor type
At first glance it seems that a lot of these are separating out cNFs (i.e. mast cell signaling) from other types. However, I’m getting the same error I get in notebook number 11, so am unsure about how to proceed.
#this is a failed attempt to group by tumor type
#with.sig<-counts%>%ungroup()%>%subset(gene%in%top.genes$Hugo_Symbol)%>%
# group_by(latent_var,tumorType,gene)%>%
# mutate(pval=t.test(value~status)$p.value)%>%
# ungroup()%>%
# group_by(latent_var)%>%
# mutate(corP=p.adjust(pval))%>%ungroup()%>%
# select(latent_var,tumorType,gene,pval,corP)%>%distinct()
#sig.vals<-subset(with.sig,corP<0.05)
#DT::datatable(sig.vals)